A lot of good feedback here. As I said at the beginning, this is just something I've been thinking about. I don't really want to go out and buy a brand new heatsink that I know won't fit, just to see if the mod will work. But I've worked with copper tubing before, so I know it can be bent if careful. I just don't know how that affects the function of the system.
...the pipes will cease to work if you cut, puncture or kink them.
Do you mean "cease to work" altogether, or just won't work past the kink? say I need to remove 5 fins and the ends of the heatpipes stuck past the top fin by 4mm. If i pinch off the heatpipes 4mm from the new top fin and just fold them over (making sure not to puncture them), it seems that it would still work fine, unless there is something about the inner workings of heatpipes that I'm missing.
BTW, anyone know where I might be able to get old, used, or otherwise dirt cheap heatpipes to experiment with?